Skip to main content
SpringerLink
Log in

Low-volume amplification on chemically structured chips using the PowerPlex16 DNA amplification kit

  • Technical Note
  • Published:
International Journal of Legal Medicine Aims and scope Submit manuscript

Abstract

In forensic DNA analysis, improvement of DNA typing technologies has always been an issue. It has been shown that DNA amplification in low volumes is a suitable way to enhance the sensitivity and efficiency of amplification. In this study, DNA amplification was performed on a flat, chemically structured glass slide in 1-μl reaction volumes from cell line DNA contents between 1,000 and 4 pg. On-chip DNA amplification reproducibly yielded full allelic profiles from as little as 32 pg of template DNA. Applicability on the simultaneous amplification of 15 short tandem repeats and of a segment of the Amelogenin gene, which are routinely used in forensic DNA analysis, is shown. The results are compared to conventional in-tube amplification carried out in 25-μl reaction volumes.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3

Similar content being viewed by others

References

  1. Eichmann C, Berger B, Reinhold M, Lutz M, Parson W (2004) Canine-specific STR typing of saliva traces on dog bite wounds. Int J Legal Med 118:337–342

    Article  PubMed  Google Scholar 

  2. Lutz-Bonengel S, Sänger T, Pollak S, Szibor R (2004) Different methods to determine length heteroplasmy within the mitochondrial control region. Int J Legal Med 118:274–281

    Article  PubMed  Google Scholar 

  3. Pfeiffer H, Lutz-Bonengel S, Pollak S, Fimmers R, Baur MP, Brinkmann B (2004) Mitochondrial DNA control region diversity in hairs and body fluids of monozygotic triplets. Int J Legal Med 118:71–74

    Article  PubMed  Google Scholar 

  4. Schlenk J, Seidl S, Braunschweiger G, Betz P, Lederer T (2004) Development of a 13-locus PCR multiplex system for paternity testing. Int J Legal Med 118:55–61

    Article  PubMed  CAS  Google Scholar 

  5. Zehner R, Amendt J, Schütt S, Sauer J, Krettek R, Povolný D (2004) Genetic identification of forensically important flesh flies (Diptera: Sarcophagidae). Int J Legal Med 118:245–247

    Article  PubMed  Google Scholar 

  6. Calzada P, Suárez I, García S et al (2005) The Fang population of Equatorial Guinea characterised by 15 STR-PCR polymorphisms. Int J Legal Med 119:107–110

    Article  PubMed  CAS  Google Scholar 

  7. Mullis KB, Faloona FA (1987) Specific synthesis of DNA in vitro via a polymerase-catalyzed chain reaction. Methods Enzymol 155:350–355

    Google Scholar 

  8. Jeffreys AJ, Wilson V, Neumann R, Keyte J (1988) Amplification of human minisatellites by the polymerase chain reaction: towards DNA fingerprinting of single cells. Nucleic Acids Res 16:10953–10971

    Article  PubMed  CAS  Google Scholar 

  9. Edwards A, Civitello A, Hammond HA, Caskey CT (1991) DNA typing and genetic mapping with trimeric and tetrameric tandem repeats. Am J Hum Genet 49:746–756

    PubMed  CAS  Google Scholar 

  10. Lygo JE, Johnson PE, Holdaway DJ et al (1994) The validation of short tandem repeat (STR) loci for use in forensic casework. Int J Legal Med 107:77–89

    Article  PubMed  CAS  Google Scholar 

  11. Junge A, Lederer T, Braunschweiger G, Madea B (2003) Validation of the multiplex kit genRESMPX-2 for forensic casework analysis. Int J Legal Med 117:317–325

    Article  PubMed  CAS  Google Scholar 

  12. Budowle B, Allard MW, Wilson MR, Chakraborty R (2003) Forensics and mitochondrial DNA: applications, debates, and foundations. Annu Rev Genomics Hum Genet 4:119–141

    Article  PubMed  CAS  Google Scholar 

  13. Szibor R, Krawczak M, Hering S, Edelmann J, Kuhlisch E, Krause D (2003) Use of X-linked markers for forensic purposes. Int J Legal Med 117:67–74

    PubMed  CAS  Google Scholar 

  14. Holland MM, Fisher DL, Mitchell LG et al (1993) Mitochondrial DNA sequence analysis of human skeletal remains: identification of remains from the Vietnam War. J Forensic Sci 38:542–553

    PubMed  CAS  Google Scholar 

  15. Pfeiffer H, Huhne J, Ortmann C, Waterkamp K, Brinkmann B (1999) Mitochondrial DNA typing from human axillary, pubic and head hair shafts—success rates and sequence comparisons. Int J Legal Med 112:287–290

    Article  PubMed  CAS  Google Scholar 

  16. Butler JM, Shen Y, McCord BR (2003) The development of reduced size STR amplicons as tools for analysis of degraded DNA. J Forensic Sci 48:1054–1064

    PubMed  CAS  Google Scholar 

  17. Parson W, Niederstätter H, Brandstätter A, Berger B (2003) Improved specificity of Y-STR typing in DNA mixture samples. Int J Legal Med 117:109–114

    PubMed  Google Scholar 

  18. Schmalzing D, Koutny L, Salas-Solano O, Adourian A, Matsudaira P, Ehrlich D (1999) Recent developments in DNA sequencing by capillary and microdevice electrophoresis. Electrophoresis 20:3066–3077

    Article  PubMed  CAS  Google Scholar 

  19. Hahner S, Schneider A, Ingendoh A, Mosner J (2000) Analysis of short tandem repeat polymorphisms by electrospray ion trap mass spectrometry. Nucleic Acids Res 28:E82

    Article  PubMed  CAS  Google Scholar 

  20. Pastinen T, Raitio M, Lindroos K, Tainola P, Peltonen I, Syvanen AC (2000) A system for specific, high-throughput genotyping by allele-specific primer extension on microarrays. Genome Res 10:1031–1042

    Article  PubMed  CAS  Google Scholar 

  21. Shinka T, Naroda T, Tamura T, Sasahara K, Nakahori Y (2001) A rapid and simple method for sex identification by heteroduplex analysis, using denaturing high-performance liquid chromatography (DHPLC). J Hum Genet 46:263–266

    Article  PubMed  CAS  Google Scholar 

  22. Underhill PA, Passarino G, Lin AA et al (2001) The phylogeography of Y chromosome binary haplotypes and the origins of modern human populations. Ann Hum Genet 65:43–62

    Article  PubMed  CAS  Google Scholar 

  23. Hahner S, Schmidt U, Kiehne A, Wunderlich D, Ingendoh A, Fröhlich T (2003) Mass spectrometric analysis of human microsatellite markers. Int Congr Ser 1239:31–38

    Google Scholar 

  24. Kricka LJ, Wilding P (2003) Microchip PCR. Anal Bioanal Chem 377:820–825

    Article  PubMed  CAS  Google Scholar 

  25. Gaines ML, Wojtkiewicz PW, Valentine JA, Brown CL (2002) Reduced volume PCR amplification reactions using the AmpFlSTR Profiler Plus kit. J Forensic Sci 47:1224–1237

    PubMed  CAS  Google Scholar 

  26. Liu RH, Yang J, Lenigk R, Bonanno J, Grodzinski P (2004) Self-contained, fully integrated biochip for sample preparation, polymerase chain reaction amplification, and DNA microarray detection. Anal Chem 76:1824–1831

    Article  PubMed  CAS  Google Scholar 

  27. Børsting C, Sanchez JJ, Morling N (2004) Multiplex PCR, amplicon size and hybridization efficiency on the NanoChip electronic microarray. Int J Legal Med 118:75–82

    Article  PubMed  Google Scholar 

  28. Mitnik L, Carey L, Burger R et al (2002) High-speed analysis of multiplexed short tandem repeats with an electrophoretic microdevice. Electrophoresis 23:719–726

    Article  PubMed  CAS  Google Scholar 

  29. Gulliksen A, Solli L, Karlsen F, Rogne H, Hovig E, Nordstrom T, Sirevag R (2004) Real-time nucleic acid sequence-based amplification in nanoliter volumes. Anal Chem 76:9–14

    Article  PubMed  CAS  Google Scholar 

  30. Huang Y, Shirajian J, Schroder A, Yao Z, Summers T, Hodko D, Sosnowski R (2004) Multiple sample amplification and genotyping integrated on a single electronic microarray. Electrophoresis 25:3106–3116

    Article  PubMed  CAS  Google Scholar 

  31. Sobrino B, Carracedo A (2005) SNP typing in forensic genetics. Methods Mol Biol 297:107–126

    PubMed  CAS  Google Scholar 

  32. Radtkey R, Feng L, Muralhidar M et al (2000) Rapid, high fidelity analysis of simple sequence repeats on an electronically active DNA microchip. Nucleic Acids Res 28:E17

    Article  PubMed  CAS  Google Scholar 

  33. Goedecke N, McKenna B, El-Difrawy S, Carey L, Matsudaira P, Ehrlich D (2004) A high-performance multilane microdevice system designed for the DNA forensics laboratory. Electrophoresis 25:1678–1686

    Article  PubMed  CAS  Google Scholar 

  34. Hagen-Mann K, Zacher T, Khanaga O, Baukloh V, Mann W, Schön U (2005) Molekularbiologische Analyse einzelner Genomäquivalente. Med Genet (in press)

Download references

Acknowledgements

We greatly acknowledge the excellent laboratory assistance of Tanja Schmitt (Alopex GmbH), who carried out the on-chip amplification reactions.

Author information

Authors and Affiliations

  1. Institute of Legal Medicine, Albert Ludwig University Freiburg, Albertstrasse 9, 79104, Freiburg, Germany

    Ulrike Schmidt, Sabine Lutz-Bonengel, Hans-Joachim Weisser, Timo Sänger & Stefan Pollak

  2. Alopex GmbH, Fritz-Hornschuch-Strasse 9, 95326, Kulmbach, Germany

    Ulrike Schön, Thomas Zacher & Wolfgang Mann

Authors
  1. Ulrike Schmidt
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Sabine Lutz-Bonengel
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Hans-Joachim Weisser
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Timo Sänger
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Stefan Pollak
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Ulrike Schön
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Thomas Zacher
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Wolfgang Mann
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Ulrike Schmidt.

Additional information

U. Schmidt and S. Lutz-Bonengel contributed equally to this work.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Schmidt, U., Lutz-Bonengel, S., Weisser, HJ. et al. Low-volume amplification on chemically structured chips using the PowerPlex16 DNA amplification kit. Int J Legal Med 120, 42–48 (2006). https://doi.org/10.1007/s00414-005-0041-2

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00414-005-0041-2

Keywords

Search

Navigation